The SEA-PHAGES Program

SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester, discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses, but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses.

The program aims to increase undergraduate interest and retention in the biological sciences through immediate immersion in authentic, valuable, yet accessible research. By finding and naming their own bacteriophages, students develop a sense of project ownership and have a ready-made personal research project at a fraction of the cost of traditional apprentice-based research programs. Some of the positive effects of the SEA-PHAGES program have been reported here.

SEA-PHAGES is jointly administered by Graham Hatfull's group at the University of Pittsburgh and the Howard Hughes Medical Institute's Science Education division.

A new study appearing this week in the scientific journal eLIFE about the rapid evolution of small viruses that infect bacteria includes 59 University of Colorado Boulder co-authors, all of whom conducted research for the paper as freshmen....read more

It is not often that a freshman in college is approached and commended for research by a Nobel Prize winner, but that is exactly what happened to Archer City graduate, London Steele, now a freshman at Baylor University....read more

It was the summer that the freshmen ruled the sequencer.
Technically, the six William & Mary students who logged heavy lab time with a state-of-the-art Ion Torrent gene sequencer had finished their freshman year and therefore did their summer work as rising sophomores....read more

An agar plate lies still. Omnicron has destroyed the layer of bacteria inside the plate, leaving plaques or dark holes 2 mm in diameter. Omnicron is a virus replicating itself inside the plate. The discovery of this virus belongs to Tasha Baer, a Florida Gulf Coast University student from the 2013-14 Virus Hunters course....read more

Sydney Dishman’s new pet isn’t cute and certainly isn’t something you’d want to cuddle with. But she feels good just thinking about it.
Her “pet” is named Rex16, after the Queens University of Charlotte mascot and her year of graduation. Rex16 is a bacteriophage species she discovered while completing her honors research thesis, investigating bacteriophages in local soil samples....read more

We know that bacteriophages are viruses that infect and replicate within bacteria. We know that they are the most abundant organisms on Earth. But we don't know much about their genetic architecture....read more

After sifting through soil samples collected from across Massachusetts, then drilling down to analyze the DNA of viruses they found, a team of undergraduates at Worcester Polytechnic Institute (WPI) hit pay dirt—three potentially novel viruses....
read more

Sixteen first-years watched with excitement as their screens loaded the sequence of 59,625 nucleic acids that comprise the DNA of “Job42,” the virus a student in their class had discovered, isolated and named during the fall semester.
“Each of them codes for something,” said Jordan Rego...read more

Surrounded by only her thoughts and glass beekers, one Cabrini student spends much of her time diligently working in the Iadarola Science Center. Katie Mageeney, senior biology major and math and chemistry minor, is anything but an average student.
“Katie is definitely dedicated to her lab work,”...read more

The 10 Austin Peay State University students in Dr. Sergei Markov’s junior- and senior-level biology classes this semester are taking advantage of a unique research opportunity that could help lead to medical breakthroughs.read more

Say the word "virus" and most people think of disease -- something to be avoided at all costs.
However, at UNLV, students are getting their hands dirty to discover something that could keep us healthy. read more

The scientific journal eLife published a paper on viruses last month—specifically, the genetics of bacteriophages: viruses that infect, and replicate within, bacteria. By sequencing the genomes of individual bacteriophages, or phages, the authors were able to glean information about the genetic makeup of the viruses more broadly....
read more

“The goal of the course, part of a national pedagogical program, is to get students doing research early, so they can see what it’s like and learn the scientific process,” explains Dr. Edgington, Associate Professor of Biology.read more

It's sequencing season! This post contains some information on sending your SEA-PHAGES phage DNA samples to the University of Pittsburgh for sequencing. Most of the information is the same as last year, but please note that our lab has moved to a new building and the shipping address has changed.

Sample Submission Form

Please submit the information about the samples you are sending via a quick Google Form. This will help us keep track of samples, correct any spelling errors, and make sure your samples are accounted for. Please fill out a copy of this form for each sample you are submitting. The best time to fill it out is as you are getting your shipment packed, so that when your box arrives, we'll already have the information on your phages in our database. Please note whether each sample is a "Priority" or "Backup" in the Notes field, along with any other info we should have.

Quantity

Each SEA-PHAGES school may have two genomes sequenced per Bioinformatics section that it is teaching during the current academic year. We recommend that you send at least one backup sample in case one of your samples fails our QC. Please indicate any order of preference, if you have one.

Deadlines

Semester Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, November 22.

Quarter Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, January 8.

If you will have trouble meeting these deadlines for any reason, please contact Dan Russell at dar78@pitt.edu.

Guidelines for DNA

Buffer

Samples that are resuspended in TE are problematic, since the EDTA may interfere with enzymatic shearing of the DNA. You can resuspend your DNA in Elution Buffer (Tris) or in purified water.

Amount

We need a minimum of 4 µg (micrograms) of genomic DNA. If you're in the ballpark of this number but not quite there, contact Dan to see if it's okay.

Concentration

At least 40 ng/µl. Ideal is 100-300 ng/µl. If you're above 300 ng/µl please consider diluting to a workable concentration and workable volume. Shipping volumes less than 20 µl is not recommended. Keep in mind that spec-based quantifications (like Nanodrop) count all absorbance at 260 nm, not just genomic DNA, so they often overestimate the real concentration. Err on the high side of the amount of DNA you send.

Gel Picture

Please submit—either via email to dar78@pitt.edu or in the shipping box—an image of the gDNA being run on an agarose gel. We use these to look for sample integrity (not already sheared/degraded) and purity (no RNA).

Labeling

Please clearly label the tubes you are sending with the name of the phage as it appears on PhagesDB. Don't label tubes using student's initials only, or other ambiguous names like "Phage1" or "PittPhage". If possible, put a small circular sticker on the top of the tube and write the phage name only on it.

Shipping

Packaging

We prefer standard microcentrifuge tubes, and strongly recommend wrapping the caps with Parafilm to prevent spilling or evaporation. The tubes can be packed into a 50 ml conical tube with some KimWipes to stabilize them during shipment. If shipping overnight (preferred), you can actually just send the samples at room temperature, as the DNA should be fine for 24 hours in transit. If shipping on a slower schedule, you should use cold packs. Aim for delivery to Pittsburgh on Tuesday-Friday. If shipping near holidays, please check with us about when we'll be around to receive samples.

You can include a packing slip with any information you think we should have about the enclosed phages.

Address

Additional Samples

For the past several years, the Genomics Sciences Laboratory at NC State has provided high-quality, for-cost sequencing services to schools in the SEA-PHAGES program who wish to sequence additional genomes beyond those allotted by the program. Contact Andy Baltzegar at dabaltze@ncsu.edu for pricing and details.

The Fall Faculty Hack-A-Thons is a series of one-day annotation workshops for faculty that are hosted by our SEA-PHAGES SMART Team and expedited submitters. The goal of the Hack-A-Thons are to improve faculty annotation skills across the SEA and help everyone refresh their memories before they teach the bioinformatics component in the Spring. These small group, faculty-focused workshops will either work through the annotation of one genome from the genome exchange or will focus on a particular annotation topic. Along the way, faculty will be reoriented to SEA-PHAGES bioinformatics tools, the Online Guide, annotation submission guidelines, changes from previous years, and useful forums and resources on seaphages.org.

Who should attend?

We encourage all faculty that will be leading the bioinformatics course to attend at least one of these workshops. Teaching assistants are welcome if there is space.
Cohort 12 faculty will soon attend a week-long in-depth bioinformatics training workshop. There will be some hack-a-thon sessions available as follow up for Cohort 12 trainees, but it’s not recommended to attend a Hack-A-Thon until after the workshop.

How to attend one?

These workshops will take place as in-person meetings, virtual meetings, or a combination of both. To attend one of these meetings, refer to the sign-up link below, which lists all the dates and locations for these meetings. Once all faculty have identified their top three choices, you will be contacted with additional details about the meetings. Food will be provided at in-person meetings, but travel to and from a meeting is at your own expense.

Please identify up to three workshops that you can attend, and rank your preference, by Sunday Oct 20, 2019.